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  • 1
    In: Biomolecules, MDPI AG, Vol. 13, No. 8 ( 2023-08-16), p. 1255-
    Abstract: The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free DNA) and associated epigenetic modifications (playing a key role in the tumorigenesis of different cancers) may provide useful information for patient management, by supporting the contributive value of ctDNA molecular profiling. Significantly elevated concentrations of H3K27Me3 nucleosomes were found in plasmas at the diagnosis, and during the follow-up, of NSCLC patients, compared to healthy donors (p-value 〈 0.0001). By combining the H3K27Me3 level and the ctDNA molecular profile, we found that 25.5% of the patients had H3K27Me3 levels above the cut off, and no somatic alteration was detected at diagnosis. This strongly supports the presence of non-mutated ctDNA in the corresponding plasma. During the patient follow-up, a high H3K27Me3-nucleosome level was found in 15.1% of the sample, despite no somatic mutations being detected, allowing the identification of disease progression from 43.1% to 58.2% over molecular profiling alone. Measuring H3K27Me3-nucleosome levels in combination with ctDNA molecular profiling may improve confidence in the negative molecular result for cfDNA in lung cancer at diagnosis, and may also be a promising biomarker for molecular residual disease (MRD) monitoring, during and/or after treatment.
    Type of Medium: Online Resource
    ISSN: 2218-273X
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 2163-2163
    Abstract: Introduction: Treatment options of lung cancer (LC) comprise radiotherapy, and/or combined treatment approaches, including chemotherapy, immunotherapy and targeted therapies based on the tumoral molecular profile. Following curative-intent first-line therapies, clinical surveillance involves serial CT imaging. However, such surveillance can detect only macroscopic disease recurrence and is frequently inconclusive. NGS has been utilized to help identify and monitor treatment plans. Nucleosomes, complexes of DNA and histones proteins, are released during cell death into blood circulation. Trimethylation of lysine 27 on histone H3 (H3K27Me3), catalyzed by enhancer of zeste homolog 2 (EZH2), is a crucial epigenetic process in tumorigenesis. We investigated if H3K27Me3-nucleosome concentration could be a biomarker for molecular residual disease (MRD). Patients and Methods: Plasmas were retrospectively collected from patients with advanced LC during treatment (CIRCAN’s cohort, n= 200) and from healthy donors (n=100). We carried out standard targeted NGS on paired plasmas. Samples were divided in two sub-groups based on genetical results: ctDNA negative (n=120) or positive (n=80) for presence of somatic alterations. Concentration of circulating H3K27Me3-nucleosome was measured using chemiluminescent Nu.Q® immunoassay (Belgian Volition SRL, Belgium). Results: Significantly elevated concentrations of H3K27Me3-nucleosomes were found in LC plasmas during the follow-up of patients compared to healthy donors (median 14.9 ng/ml vs 6.15 ng/ml, respectively, p & lt;0.001). In addition, H3K27Me3 levels is lower in the ctDNA-negative group compared to ctDNA-positive group (median 12.1 vs 24.8 ng/ml, respectively, p & lt;0.001). At a clinical cut-off of 14 ng/ml, 62% of samples were positive for either H3K27Me3 or ctDNA, or for both, suggesting an active disease progression compared to only 40% detection using the NGS assay alone. 38% of the patients have low levels of H3K27Me3 and were ctDNA-negative strongly suggesting a therapeutic response under treatment. Conclusions: High levels of Nu.Q® H3K27Me3 could allow physicians to detect MRD in LC patients following treatment with curative intent. This could be achieved by monitoring testing of patients at defined intervals of treatment and recovery, alongside imaging, to incorporate analyses of evolving molecular landscapes during treatment. In this setting, the H3K27Me3-nucleosome quantification, to complete the molecular exploration of cfDNA is highly encouraging, especially in advanced NSCLC, where re-tissue biopsies are impractical, expensive, and may cause undue harm. H3K27Me3-nucleosome quantification may also be useful in patient identification for specific treatments such as EZH2 inhibitor, but this requires investigation. Citation Format: Emmanuel Grolleau, Julie Candiracci, Arnaud Gauthier, Gaelle Lescuyer, David Barthelemy, Christine Haon, Florence Geiguer, Margaux Raffin, Nathalie Hardat, Julie Balandier, Rémi Rabeuf, Anne-Sophie Wozny, Guillaume Rommelaere, Claire Rodriguez-Lafrasse, Fabien Subtil, Sébastien Couraud, Marielle Herzog, Lea Payen-Gay. Circulating H3K27 nucleosomes to monitor lung cancer patients during treatment, a universal biomarker quantifying the molecular residual disease (MRD) in plasma samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2163.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 6691-6691
    Abstract: Background: Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients. We sought to validate an ultra-deep plasma Next-Generation Sequencing (NGS) assay for patients with Non-Small-Cell Lung Cancers (NSCLC) for detecting Minimal Residual Disease (MRD) following curative-intent NSCLC treatment or EGFR detection at an early stage. Patients and Methods: We carried out targeted NGS using the Plasma-SeqSensei™ Solid Cancer IVD Kit on cfDNA extracted from plasma. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis. Sensitivity and specificity for plasma detection of known oncogenic drivers were calculated. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with a custom-validated NGS assay. Results: In comparison with the OncoBEAMTM EGFR V2 kit, we observed a 75% concordance with the Plasma-SeqSensei™ Solid Cancer IVD Kit. The 25% genomic discordances were respectively observed in 5%, 7% and 13% linked to the limit of coverage of the OncoBEAMTM EGFR V2 kit, the limit of EGFR sensitivity of the Plasma-SeqSensei™ Solid Cancer IVD Kit and the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ Solid Cancer IVD Kit. In comparison with the custom-validated NGS assay, we observed a 68% concordance with the Plasma-SeqSensei™ Solid Cancer IVD Kit. The 32% genomic discordances were respectively observed in 5%, 11% and 16% linked to the limit of coverage of the Plasma-SeqSensei™ Solid Cancer IVD Kit, the limit of covered sensitivity of the custom-validated NGS assay and the additional oncodrivers analysis only covered by the custom-validated NGS assay. Benefitting from the higher coverage from targetable BRAF, KRAS, PIK3CA targetable alterations, the plasma targeted NGS Plasma-SeqSensei™ Solid Cancer IVD Kit showed 13% additional discordances with the Plasma OncoBEAMTM EGFR V2 kit. Most of these additional somatic alterations were cross-validated in our orthogonal custom-validated NGS assay, used in the routine management of patients. The custom-validated NGS assay sensitivity is determined for MAF at 1%, explaining the limit of sensitivity with the Plasma-SeqSensei™ Solid Cancer IVD Kit. Conclusions: Plasma-SeqSensei™ Solid Cancer IVD Kit resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsies were inadequate for genotyping with high sensitivity and accuracy for low and high cfDNA inputs. Citation Format: David Barthelemy, Emmanuel Grolleau, Gaelle Lescuyer, Florence Geiguer, Arnaud Gauthier, Julie Balandier, Margaux Raffin, Claire Bardel, Bruno Bouyssounouse, Claire Rodriguez-Lafrasse, Sébastien Couraud, Anne-Sophie Wozny, Lea Payen-Gay. Paired comparison of routine molecular screening of patient samples with advanced non-small cell lung cancer in circulating cell-free DNA using OncoBEAMTM EGFR V2, targeted next-generation sequencing Plasma-SeqSensei™ Solid Cancer IVD Kit and custom-validated NGS assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6691.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 1013-1013
    Abstract: Background: In patients with advanced lung adenocarcinoma cancers, a subset can be cured by radiotherapy, and/or combined regimens, including chemotherapy, immunotherapy, or targeted therapies based on somatic molecular profiling. Nucleosomes are basic elements of chromatin, composed of 147bp DNA wrapped around an octamer of histones. Cell-free DNA (cfDNA) and nucleosomes are released into the bloodstream upon cell death. In addition to genetic somatic alterations, epigenetic modifications are found to play a key role in tumorigenesis of different cancers. The trimethylated histone H3 at lysine 27 (H3K27Me3) is well known as a transcription-repressive mark and proven to be involved in tumorigenesis, cell cycle progression and proliferation dysregulation. However, the concentration of circulating nucleosomes, as a biomarker of the contributive value of circulating tumor DNA (ctDNA) molecular profiling in patient management at diagnosis has not previously been investigated. Patients and Methods: Plasmas were retrospectively collected from patients with NSCLC at initial diagnosis before treatment (CIRCAN’s cohort, N= 198) and from healthy donors (N=100). We carried out targeted next-generation sequencing (NGS) on paired plasmas. Samples were divided in two sub-groups based on the genetic results: ctDNA negative or positive for presence of somatic alterations. The concentration of global circulating nucleosomes as well as specific methylated marks: H3K4Me2-, H3K9Me3-, H3K27Me3- or H3K36Me3-nucleosomes were measured using chemiluminescent Nu.Q® immunoassays (Belgian Volition SRL, Belgium). Results: Among all the different nucleosome forms evaluated, the highest coefficient correlations with cfDNA concentration were observed for H3K27Me3-nucleosomes (r=0.72, p & lt;0.0001). At a cut-off of 14 ng/ml of H3K27Me3-nucleosomes Nu.Q® assay showed a sensitivity of 69.2% (n=137) at 95% specificity for lung cancers vs healthy donors (AUC= 0.92). Interestingly, by combining H3K37Me3 level and ctDNA molecular profile, we found a contributive diagnostic value of molecular profiling results in 77% of the plasmas versus only 40% using NGS alone as per current practice. 32% of plasmas were positive for both H3K27Me3 and ctDNA; 37% are H3K27Me3-positive but ctDNA-negative; 8% of the samples were ctDNA-positive/H3K27Me3-negative and 23% are negative for both H3K27Me3 and ctDNA. Conclusions: High levels of Nu.Q® H3K27Me3 and the absence of detecting somatic alterations strongly support the presence of non-mutated ctDNA in the corresponding plasma. This greatly improves the confidence in the negative molecular results in cfDNA in LC. This may allow the indication of individualized therapeutic regimens with a short-time medical decision and may reduce invasive tissue re-biopsies. Citation Format: Arnaud Gauthier, Julie Candiracci, Emmanuel Grolleau, Gaelle Lescuyer, David Barthelemy, Christine Haon, Florence Geiduer, Margaux Raffin, Nathalie Hardat, Julie Balandier, Rémi Rabeuf, Anne-Sophie Wozny, Claire Rodriguez-Lafrasse, Guillaume Rommelaere, Fabien Subtil, Sébastien Couraud, Marielle Herzog, Lea Payen-Gay. Circulating H3K27 methylated nucleosome concentration in lung cancer improves the contributive value of ctDNA molecular profiling result at diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1013.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 5
    In: Cancers, MDPI AG, Vol. 15, No. 5 ( 2023-03-03), p. 1574-
    Abstract: Introduction: Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80–85% of all lung cancers. Approximately 10–50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. Patients and Methods: Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. Results: In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. Conclusions: The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.
    Type of Medium: Online Resource
    ISSN: 2072-6694
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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